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Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock-A Simulation Study

Citation

Holland, BR and Penny, D and Hendy, MD, Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock-A Simulation Study, Systematic Biology, 52, (2) pp. 229-238. ISSN 1063-5157 (2003) [Refereed Article]


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The definitive publisher-authenticated version is available online at: www.oxfordjournals.org

DOI: doi:10.1080/10635150390192771

Abstract

We conducted a simulation study of the phylogenetic methods UPGMA, neighbor joining, maximum parsimony, and maximum likelihood for a five-taxon tree under a molecular clock. The parameter space included a small region where maximum parsimony is inconsistent, so we tested inconsistency correction for parsimony and distance correction for neighbor joining. As expected, corrected parsimony was consistent. For these data, maximum likelihood with the clock assumption outperformed each of the other methods tested. The distance-based methods performed marginally better than did maximum parsimony and maximum likelihood without the clock assumption. Data correction was generally detrimental to accuracy, especially for short sequence lengths. We identified another region of the parameter space where, although consistent for a given method, some incorrect trees were each selected with up to twice the frequency of the correct (generating) tree for sequences of bounded length. These incorrect trees are those where the outgroup has been incorrectly placed. In addition to this problem, the placement of the outgroup sequence can have a confounding effect on the ingroup tree, whereby the ingroup is correct when using the ingroup sequences alone, but with the inclusion of the outgroup the ingroup tree becomes incorrect.

Item Details

Item Type:Refereed Article
Keywords:Equal rates; inconsistency; maximum likelihood; maximum parsimony; misleading zones; neighbor joining; outgroup rooting; UPGMA
Research Division:Mathematical Sciences
Research Group:Applied Mathematics
Research Field:Biological Mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Holland, BR (Associate Professor Barbara Holland)
ID Code:62978
Year Published:2003
Web of Science® Times Cited:88
Deposited By:Mathematics
Deposited On:2010-03-31
Last Modified:2010-04-30
Downloads:0

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